Genome-wide gene-environment interaction testing results summary
Summary Manhattan plots
- Dotted line corresponds to genome-wide significance (p = 5e-8)
- “Joint” corresponds to the joint test of genetic main and interaction effect
- “Marginal” corresponds to the genetic main effect from a model adjusted for the exposure but not including a genetic interaction term
Interaction test
- A simple distance-based pruning method is used here, with total window size of 500 kb (250 kb on each side).
| index_var | chr | pos | P_int | G-W interaction effect | P_joint | P_marginal |
|---|---|---|---|---|---|---|
| rs12136785 | 1 | 89478687 | 4.7e-06 | FALSE | 6.70e-06 | 0.0884292 |
| rs75242550 | 2 | 47777458 | 9.6e-06 | FALSE | 3.74e-05 | 0.4243720 |
| rs12197749 | 6 | 146536288 | 3.1e-06 | FALSE | 1.92e-05 | 0.3766780 |
| 7:7343876_CA_C | 7 | 7343876 | 2.4e-06 | FALSE | 7.80e-06 | 0.3709310 |
| rs4128327 | 8 | 110032847 | 3.4e-06 | FALSE | 1.12e-05 | 0.0793897 |
| rs555728622 | 10 | 100281893 | 5.8e-06 | FALSE | 2.62e-05 | 0.8744820 |
| 11:6801573_CAAA_C | 11 | 6801573 | 9.1e-06 | FALSE | 5.60e-06 | 0.1917850 |
| rs61944504 | 13 | 27321494 | 2.3e-06 | FALSE | 1.14e-05 | 0.3039250 |
| rs4793425 | 17 | 70299527 | 2.9e-06 | FALSE | 8.40e-06 | 0.8687370 |
| rs55690660 | 17 | 72352686 | 6.5e-06 | FALSE | 3.83e-05 | 0.5641650 |
| rs1053744 | 22 | 50885775 | 6.1e-06 | FALSE | 1.33e-05 | 0.1111860 |
| index_var | chr | pos | P_marginal |
|---|---|---|---|
| rs116777618 | 1 | 205431181 | 2.5e-06 |
| rs12727804 | 1 | 91733994 | 0.0e+00 |
| rs7367177 | 1 | 158045407 | 8.0e-06 |
| rs758983573 | 1 | 14152154 | 4.8e-06 |
| rs35489748 | 2 | 2957848 | 8.4e-06 |
| rs560385512 | 2 | 179548951 | 4.4e-06 |
| rs115093875 | 2 | 188943739 | 2.1e-06 |
| 2:202679672_AT_A | 2 | 202679672 | 1.9e-06 |
| rs112916110 | 2 | 70820996 | 8.5e-06 |
| rs12465135 | 2 | 34017430 | 1.0e-07 |
| 5:125873847_CAAAAAAAAAAAAAA_C | 5 | 125873847 | 3.9e-06 |
| rs17051780 | 6 | 124710492 | 8.6e-06 |
| rs79981382 | 6 | 64606946 | 5.6e-06 |
| rs71715757 | 6 | 164375525 | 4.7e-06 |
| rs745604245 | 6 | 154800208 | 4.1e-06 |
| rs145332204 | 7 | 148066266 | 2.7e-06 |
| rs703413 | 10 | 119311377 | 9.2e-06 |
| 11:1796572_AG_A | 11 | 1796572 | 3.5e-06 |
| rs11612110 | 12 | 9352791 | 8.4e-06 |
| rs36064217 | 12 | 83803246 | 1.8e-06 |
| 12:116391621_TA_T | 12 | 116391621 | 0.0e+00 |
| rs9545832 | 13 | 82247081 | 2.5e-06 |
| rs61975598 | 14 | 92843276 | 6.7e-06 |
| rs76787529 | 14 | 78868119 | 9.0e-06 |
| rs1243596 | 14 | 21072640 | 5.8e-06 |
| rs66638200 | 14 | 33621296 | 4.7e-06 |
| rs35872736 | 15 | 45618301 | 1.5e-06 |
| rs4300625 | 15 | 92257885 | 2.6e-06 |
| rs73365896 | 15 | 29766707 | 4.6e-06 |
| rs73531463 | 16 | 6310835 | 7.0e-07 |
| rs61190547 | 16 | 24032297 | 4.2e-06 |
| rs76839250 | 16 | 90051269 | 6.0e-07 |
| rs200513128 | 17 | 18392377 | 4.2e-06 |
| rs16973407 | 19 | 39913558 | 3.0e-06 |
Joint test
| index_var | chr | pos | P_joint | Genome-wide joint locus | Genome-wide marginal locus |
|---|---|---|---|---|---|
| rs12727804 | 1 | 91733994 | 2.87e-08 | TRUE | TRUE |
| rs17544265 | 1 | 215152131 | 4.02e-08 | TRUE | FALSE |
| rs1491690 | 3 | 70131341 | 9.64e-09 | TRUE | FALSE |
| rs4435599 | 10 | 42390234 | 3.42e-08 | TRUE | FALSE |
| rs190316617 | 11 | 1797388 | 5.61e-09 | TRUE | TRUE |
| rs148035207 | 16 | 6330954 | 6.62e-09 | TRUE | FALSE |
| rs73157943 | 22 | 25333267 | 3.01e-09 | TRUE | FALSE |
| Parameter | Value |
|---|---|
| chromosome_col | CHR |
| position_col | POS |
| ref_allele_col | Non_Effect_Allele |
| alt_allele_col | Effect_Allele |
| allele_freq_col | AF |
| beta_interaction_col | Beta_Interaction_1 |
| p_interaction_col | P_Value_Interaction |
| p_joint_col | P_Value_Joint |
| p_marginal_col | P_Value_Marginal |
| gw_threshold | 5e-8 |
| prune_threshold_int | 1e-5 |
| prune_threshold_joint | 5e-8 |
| prune_locus_width | 500000 |
| GEM_file | sex_int_res_full |
| variant_id_col | RSID |
| maf_filter | 0.05 |